Disease Clusters?
Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.
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Cluster 280
6
Diseases
8
Unique genes
0.204
Avg. similarity score
14q11.2 microduplication syndrome
Most-connected disease (4 links)
Disease
Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details ·
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14q11.2 microduplication syndrome
Congenital ptosis
Chromodomain helicase dna binding protein 8 overgrowth syndrome
Intellectual developmental disorder autism dysmorphic
Congenital corneal opacity
FOXG1 disorder
Member diseases (most connected first ‐ the cluster's core)
| Disease ⇵ | Connections in cluster ⇵ | Significant partners ⇵ | Curated genes ⇵ |
|---|---|---|---|
| 14q11.2 microduplication syndrome | 4 | 4 | 3 |
| Congenital ptosis | 4 | 4 | 5 |
| Chromodomain helicase dna binding protein 8 overgrowth syndrome | 3 | 3 | 1 |
| Intellectual developmental disorder autism dysmorphic | 3 | 3 | 2 |
| Congenital corneal opacity | 1 | 1 | 1 |
| FOXG1 disorder | 1 | 1 | 1 |
Top shared genes (genes linked to 2+ member diseases)
| Gene ⇵ | Member diseases ⇵ | Linked diseases |
|---|---|---|
| CHD8 | 4 / 6 | 14q11.2 microduplication syndrome, Chromodomain helicase dna binding protein 8 overgrowth syndrome, Congenital ptosis, Intellectual developmental disorder autism dysmorphic |
| FOXG1 | 2 / 6 | 14q11.2 microduplication syndrome, FOXG1 disorder |
| ZFHX4 | 2 / 6 | Congenital corneal opacity, Congenital ptosis |
What do these columns mean?
- Connections in cluster
- How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
- Significant partners
- How many of those links are statistically significant (FDR q < 0.05).
- Curated genes
- Distinct curated genes linked to that disease in GeDiPNet.
- Member diseases (Top shared genes)
- How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
- Overlap genes (x / y)
- x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
- Cluster gene count
- Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
- Fold enrichment
- Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
- P-value / FDR q-value
- Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
- Shared genes (Pairs within this cluster)
- Number of curated genes the two diseases in that row have in common.
- Similarity score (Pairs within this cluster)
- Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.
Enriched Pathways (why this cluster is grouped, biologically)
None of these pathways reaches significance (all FDR q ≥ 0.05). They’re the best candidates found, but treat them as weak evidence for why this cluster groups together.
| Pathway ⇵ | Source ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| FOXO-mediated transcription of cell cycle genes | Reactome | 1 / 11 | 136× | 7.31e-3 | 5.62e-2 |
| Virion - Lassa virus and SFTS virus | KEGG | 1 / 17 | 88.3× | 1.13e-2 | 7.36e-2 |
| RHO GTPases activate PAKs | Reactome | 1 / 23 | 65.3× | 1.52e-2 | 8.78e-2 |
| Deactivation of the beta-catenin transactivating complex | Reactome | 1 / 42 | 35.7× | 2.76e-2 | 1.23e-1 |
| Collagen chain trimerization | Reactome | 1 / 44 | 34.1× | 2.89e-2 | 1.26e-1 |
| COPI-independent Golgi-to-ER retrograde traffic | Reactome | 1 / 51 | 29.4× | 3.35e-2 | 1.37e-1 |
| Collagen degradation | Reactome | 1 / 52 | 28.9× | 3.41e-2 | 1.39e-1 |
| RNA Polymerase II Transcription Elongation | Reactome | 1 / 59 | 25.4× | 3.86e-2 | 1.49e-1 |
| Formation of RNA Pol II elongation complex | Reactome | 1 / 61 | 24.6× | 3.99e-2 | 1.52e-1 |
| TP53 Regulates Transcription of DNA Repair Genes | Reactome | 1 / 65 | 23.1× | 4.25e-2 | 1.57e-1 |
| Collagen biosynthesis and modifying enzymes | Reactome | 1 / 67 | 22.4× | 4.38e-2 | 1.59e-1 |
| RNA Polymerase II Pre-transcription Events | Reactome | 1 / 84 | 17.9× | 5.46e-2 | 1.79e-1 |
| RAB GEFs exchange GTP for GDP on RABs | Reactome | 1 / 90 | 16.7× | 5.84e-2 | 1.86e-1 |
| Regulation of TP53 Activity through Phosphorylation | Reactome | 1 / 92 | 16.3× | 5.97e-2 | 1.88e-1 |
| Protein digestion and absorption | KEGG | 1 / 103 | 14.6× | 6.66e-2 | 1.99e-1 |
Enriched GO Terms (Biological Process, a second line of biological evidence)
| GO term ⇵ | GO ID ⇵ | Overlap genes ⇵ | Fold enrichment ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| brain development | GO:0007420 | 4 / 244 | 38.3× | 1.91e-6 | 1.38e-4 ✓ sig. |
| regulation of calcium ion-dependent exocytosis of neurotransmitter | GO:1903233 | 1 / 2 | 1,168× | 8.56e-4 | 1.36e-2 ✓ sig. |
| positive regulation of glutamate neurotransmitter secretion in response to membrane depolarization | GO:0061646 | 1 / 2 | 1,168× | 8.56e-4 | 1.36e-2 ✓ sig. |
| fourth ventricle development | GO:0021592 | 1 / 2 | 1,168× | 8.56e-4 | 1.36e-2 ✓ sig. |
| pyramidal neuron migration to cerebral cortex | GO:0021852 | 1 / 3 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| establishment of protein localization to endoplasmic reticulum membrane | GO:0097051 | 1 / 3 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| positive regulation of endoplasmic reticulum tubular network organization | GO:1903373 | 1 / 3 | 779× | 1.28e-3 | 1.75e-2 ✓ sig. |
| positive regulation of protein lipidation | GO:1903061 | 1 / 4 | 584× | 1.71e-3 | 2.07e-2 ✓ sig. |
| axon midline choice point recognition | GO:0016199 | 1 / 5 | 467× | 2.14e-3 | 2.34e-2 ✓ sig. |
| third ventricle development | GO:0021678 | 1 / 5 | 467× | 2.14e-3 | 2.34e-2 ✓ sig. |
| mitochondrion-endoplasmic reticulum membrane tethering | GO:1990456 | 1 / 8 | 292× | 3.42e-3 | 3.03e-2 ✓ sig. |
| negative regulation of fibroblast apoptotic process | GO:2000270 | 1 / 8 | 292× | 3.42e-3 | 3.03e-2 ✓ sig. |
| neuron fate determination | GO:0048664 | 1 / 8 | 292× | 3.42e-3 | 3.03e-2 ✓ sig. |
| substrate-dependent cell migration, cell extension | GO:0006930 | 1 / 10 | 234× | 4.27e-3 | 3.38e-2 ✓ sig. |
| axonogenesis involved in innervation | GO:0060385 | 1 / 10 | 234× | 4.27e-3 | 3.38e-2 ✓ sig. |
Pairs within this cluster, by significance
| Disease A ⇵ | Disease B ⇵ | Similarity score ⇵ | Shared genes ⇵ | P-value ⇵ | FDR q-value ⇵ |
|---|---|---|---|---|---|
| Chromodomain helicase dna binding protein 8 overgrowth syndrome | Intellectual developmental disorder autism dysmorphic | 0.333 | 1 | 1.30e-4 | 3.90e-4 ✓ sig. |
| 14q11.2 microduplication syndrome | Chromodomain helicase dna binding protein 8 overgrowth syndrome | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| 14q11.2 microduplication syndrome | FOXG1 disorder | 0.250 | 1 | 1.95e-4 | 5.28e-4 ✓ sig. |
| Chromodomain helicase dna binding protein 8 overgrowth syndrome | Congenital ptosis | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| Congenital corneal opacity | Congenital ptosis | 0.167 | 1 | 3.25e-4 | 7.58e-4 ✓ sig. |
| 14q11.2 microduplication syndrome | Intellectual developmental disorder autism dysmorphic | 0.200 | 1 | 3.90e-4 | 8.52e-4 ✓ sig. |
| Congenital ptosis | Intellectual developmental disorder autism dysmorphic | 0.143 | 1 | 6.49e-4 | 1.22e-3 ✓ sig. |
| 14q11.2 microduplication syndrome | Congenital ptosis | 0.125 | 1 | 9.74e-4 | 1.64e-3 ✓ sig. |